多位点序列分型(multilocus sequence typing,MLST)是一种基于核酸序列测定的细菌分型方法。这种方法通过PCR扩增多个管家基因内部片段并测定其序列,分析菌株的变异。
依赖conda安装
conda install -c conda-forge -c bioconda -c defaults mlst mlst contigs.fa contigs.fa neisseria 11149 abcZ(672) adk(3) aroE(4) fumC(3) gdh(8) pdhC(4) pgm(6) mlst genomes/* genomes/6008.fna saureus 239 arcc(2) aroe(3) glpf(1) gmk_(1) pta_(4) tpi_(4) yqil(3) genomes/strep.fasta.gz ssuis 1 aroA(1) cpn60(1) dpr(1) gki(1) mutS(1) recA(1) thrA(1) genomes/NC_002973.gbk lmonocytogenes 1 abcZ(3) bglA(1) cat(1) dapE(1) dat(3) ldh(1) lhkA(3) genomes/L550.gbk.bz2 leptospira 152 glmU(26) pntA(30) sucA(28) tpiA(35) pfkB(39) mreA(29) caiB(29) mlst --scheme neisseria NM* NM003.fa neisseria 4821 abcZ(222) adk(3) aroE(58) fumC(275) gdh(30) pdhC(5) pgm(255) NM005.gbk neisseria 177 abcZ(7) adk(8) aroE(10) fumC(38) gdh(10) pdhC(1) pgm(20) NM011.fa neisseria 11 abcZ(2) adk(3) aroE(4) fumC(3) gdh(8) pdhC(4) pgm(6) NMC.gbk.gz neisseria 8 abcZ(2) adk(3) aroE(7) fumC(2) gdh(8) pdhC(5) pgm(2) mlst --legacy --scheme neisseria *.fa FILE SCHEME ST abcZ adk aroE fumC gdh pdhC pgm NM003.fa neisseria 11 2 3 4 3 8 4 6 NM009.fa neisseria 11149 672 3 4 3 8 4 6 MN043.fa neisseria 11 2 3 4 3 8 4 6 NM051.fa neisseria 11 2 3 4 3 8 4 6 NM099.fa neisseria 1287 2 3 4 17 8 4 6 NM110.fa neisseria 11 2 3 4 3 8 4 6
链接:Mlst官网
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